Mary
by MacGateFan
Summary: Sequel to With Friends Like These. A visit to the mainland. Sounds innocent enough, right? Shep angst!


Title: Mary  
Rating: PG  
Author: MacGateFan  
Disclaimers: Nope, not mine except for the storyline and Mary Sheppard.  
Note from the Author: Please bear with me for Chapter 8 of Secrets of the Mind. For some reason parts of it didn't save and I had to rewrite what I had. It's not an easy task. I hope to have something up by Tuesday at the latest. Thanks again for reading!

* * *

It wasn't that she didn't have what she wanted growing up. It wasn't that she didn't love the people who she came to know as her parents. It was the fact that these said parents lied to her. It was the fact that her real parents lives were destroyed by people whom they didn't even know.

Mary tried hard to remember her life before she whisked away and told her real parents didn't want her. Ever since she had found her Dad, I had begun having dreams, or memories of the past.

Mary's parents did everything for her. They watched movies with me, her Dad taught her how to ride a tricycle, and they both loved taking her to the amusement park. She remembered that fateful day she was taken.

She remembered feeling so lost. She remembered wishing she had just listened to her Dad when he said it was time go home. She remembered wishing that ride never existed so she wouldn't have disobeyed him.

Okay, she needed to calm down. What's done is done. The important thing is that Mary Sheppard, found her Dad and is no longer living a lie. In fact, she was living in a mythological city.

Atlantis.

People would probably think Mary was crazy. She would have too if she hadn't seen it with her own eyes. If she hadn't been brought there. Mary was in a whole new galaxy and on a whole new planet. The only person she missed from Earth was her best friend, Jenna. Oh, she would so love this place!

Mary glanced up at Dr. McKay as he prattled on about physics. She knew she should be listening, but she couldn't help the fact that his lab has a window and an absolutely awesome view of the city.

"Mary." She heard a finger snapping and blinked, looking up at Dr. McKay as innocently as she could. "What is the method of successive substitution?"

Mary was about to reply when John entered. "The method of solving problems of simultaneous congruences by using the definition of the congruence equation."

The look on Dr. McKay's face was priceless. Clearly he had no idea John would know the answer to that. Mary grinned at her Dad, who was obviously enjoying Dr. McKay's lack of speech right now.

"What?" he asked.

"You think you're so smart!"

"Look who's talking!"

"At least I have the decency to use my smartness to save our asses. What have you done with it?"

"Do I have to remind you of Dagan?"

Dr. McKay shifted uncomfortably. "No." There was a pause and finally, "So why didn't you join MENSA?"

"McKay."

He finally took the hint to shut up and looked back at Mary. She smiled and shook her head. The pair of them were like little kids. She understood why Elizabeth was annoyed daily by their little disagreements.

"Ready to go?" Dad asked.

"Definitely!"

John was taking Mary to the mainland for a small vacation. Carson was also ordering Elizabeth to join them for the R&R. Mary was happy. She really liked Elizabeth and could tell her Dad did too. Now she just had to figure out a way to get them to admit it to one another.

John watched in contentment as Mary ran after Jinto. She taught him how to play tag. He couldn't believe that she was actually there.

When he first heard from Jack O'Neill that Mary was alive, he was stunned beyond belief. John never thought he'd see his little girl again. He silently wished my wife were around to see what a beautiful woman Mary was becoming.

Of course, then John remembered what I missed. He missed when Mary lost her first tooth. He missed her first day of school. He missed her graduating from grade school.

"John?"

He turned to face Elizabeth. "Are you all right?"

"Fine. Just thinking…"

"About Mary no doubt," she replied, watching the young girl as she and Jinto rushed into the woods. Mary was exactly like her Father. She was ready to help out whenever needed and she was certainly giving Rodney a run for his money in physics.

He smiled. "Yeah."

"Colonel Sheppard!" Jinto exclaimed, running over. "It's Mary, she fell!"

That immediately wiped the smile from John's face and he felt as if his lunch were about to resurface. "Where?" he asked, jumping up.

"Near the cliff where we sit to view the ocean. We were just talking and the ground gave away. I tried to catch her! I swear I did!"

John didn't reply he just ran off in the direction of the cliff, Halling right behind him. Elizabeth put her hand on Jinto's shoulder. "Don't worry. Colonel Sheppard isn't angry with you. He knows you tried your best. Right now he's just concerned for Mary."

Jinto nodded, but didn't seem convinced. Elizabeth debated whether to follow John or wait with Jinto. Looking at the boy, she saw tears coursing down his cheeks. She knelt down in front of him and wrapped her arms around him

"It's all right, Jinto. Mary will be fine."

John's heart was thundering in chest as the reached the cliff. He was almost afraid to look down. He took a deep breath and did so. Mary lay on back, her face looking out towards the water. He noticed the drop was about ten feet.

"Is there a way down there?" he asked Halling.

"None that I know of."

"Mary!!!" he called, but there was no response. John took another deep breath as he attempted to hold in his tears. "Elizabeth."

"John! Is she all right?"

"I-I don't know. We can't get to her. Grab the climbing equipment from the Jumper. I can't… I don't want to leave her in case she wakes up."

"I'll be there as soon as possible, John. Weir out."

John was pacing worriedly back and forth when Elizabeth arrived. A few of the Athosians came to help her carry the equipment. "Has she regained consciousness yet?" she asked breathlessly.

"No," John replied, taking the equipment and getting set up. "I didn't ask, but did you happen to call Carson? I'm afraid to move her when I get down there."

"Don't worry, Carson will be here shortly. Apparently so will Rodney, Ronon, and Teyla." John nodded and got to work to save his little girl.

It felt like forever before he reached Mary. She was lying so still and looked almost peaceful. "Mary," he said, kneeling next to her. "Sweetheart, it's time to get up."

Mary moaned. "Daddy?"

"Yeah, baby, I'm here. I'm not going to move you just yet. We're going to wait for Dr. Beckett to get here all right?"

"Everything hurts, Daddy."

"I know. We'll get you back to Atlantis soon, I promise." Before he could say more, she was out again. "Damn it!"

John heard Carson's voice crackle through his earpiece. Had it already been that long? "Colonel, how's Mary, son?"

"She said everything hurts."

"She's conscious then?"

"No. I mean, not anymore. Carson, is that a bad sign?" he asked worriedly.

Carson and the others appeared at the edge and John looked up when heard his friend's voice. "Not necessarily, John. Just stay calm I'll be down in a moment."

John was relieved when he saw there was just enough room for the physician to join them on the outcropping. Carson smiled sympathetically at him and knelt next to Mary. As he worked, he noticed blood coming from underneath the girl.

He didn't want to alarm John, but felt he needed to know. "John," he said. "I need you to try and wake her up for me." He nodded. "And John, I need you to be strong for Mary, but I also need you to know that's she's bleeding."

"Wh-what?" John asked.

"John."

John nodded slowly and leaned in closer to her. "Mary. Sweetheart, it's time to get up. You better hurry or Rodney's going eat the last of the blue jell-o."

"Good, Colonel. She's stirring. Mary, it's Dr. Beckett. I'm just going to do a few tests on you to before we bring you back to Atlantis. Squeeze my hand if you understand me. Good."

"Hurts, Doc," she whispered.

"I know, Love," he replied. "And that's a good sign. Your Dad and I are going to turn you onto your back now."

"O-okay."

Carson situated himself near Mary's head while John grabbed her legs. Everyone who was nearby nearly died at the cry Mary elicited as she was turned. John thought he was going to pass out when he saw the jagged rock she had landed on.

He blinked when Carson began shoving towels in hands, telling him to help stop the bleeding. "I'm sorry, Mary," he said as she whimpered under his touch.

"She's stable for now, John. We should get ready to move her." John nodded as he set to work. "Rodney, make sure the Jumper is ready for take off."

"Got it!" came Rodney's reply.

* * *

Elizabeth found John pacing back and forth in the infirmary. When he looked up at her she was surprised to see tears streaming down his pale face. John Sheppard was not one to readily share his emotions, but this time was different and she understood completely.

Elizabeth noted that his team was nearby getting their post mission check up. "John," she said.

"Carson hasn't come out yet," he responded, voice thick with emotion. "There was so much… so much blood."

"Mary will be all right!" Elizabeth told him as she place a hand on his shoulder. "She's a very strong girl thanks to her Father's genes."

"I know, but I still can't help but fear the worst."

Carson took a deep breath and walked over to John. He was usually a little more professional than he felt right now, but he had become very attached to Mary Sheppard. They all have. "She's in serious condition, John. She has a deep gash on her stomach from the rock and has lost a fair amount of blood, although that's not what I'm most concerned about.

"It's her head injury. Mary has yet to regain consciousness and there's a very real possibility that she'll slip into a coma." Carson swallowed around the lump his throat and noted John's pale features. "If she does, John, she may not wake up again. There is just too much swelling. We're going to attempt relieve some of the pressure, but I just want you to be aware of what could happen."

"Can I see her?" John asked barely above a whisper.

"Aye. Come with me, son." As Carson led John towards the isolation room they placed her in, he said. "You need to be prepared for what you're going to see. She has tubes connected to her and she's going to look pale and sick."

John nodded slowly. "Okay. I just want to see her, Doc. "

When John entered the room and saw Mary among all the wires and attached to the monitors, he was very grateful Carson was next to him because his knees gave out. The physician caught him and with the help of one of the nurses, guided John to the chair next to Mary's bed.

"Sorry," he muttered.

"No need to apologize, John," Carson said. "Why don't you take her hand, let her know you're here."

John took a deep breath. "Will she hear my if I talk to her?"

"I honestly don't know, but it definitely wouldn't hurt if you did." Carson gave John a pat on the shoulder and left room to give him some time alone with Mary.

"Hey, Mar. It's Dad. You have to fight hard, Angel. Please don't leave me so soon after we found each other. I don't know what I would do if I lost you again. You're my baby girl, my connection to your Mom. Please, Mary, come back to me!"

Unfortunately there was no external response. John just wanted to cry, but no tears would flow. Damn it why couldn't he cry?

He wanted Mary to wake up so badly. He wanted to hear her debate quantum theories with Rodney. He wanted to hear her recite foreign languages with Elizabeth. He wanted to hear her laugh and joke with him again.

"Don't leave me, Angel. Please don't leave me," John whispered. He laid his head next to her hand and drifted off into a restless sleep.

* * *

It's very warm here. Where am I? The last thing I remember was playing with Jinto on the mainland. We were going to watch the sun set.

I finally decided to open my eyes only to find that I'm floating above my beautiful new world. Okay this isn't possible, certainly not with a space suit. The only one I could be like this is because…

Oh my God!

Am I dead?

_Daddy! Daddy, where are you?_

It's so quiet in space. I should know, but it's still really creepy and I'm all by myself.

No! I don't want to be dead! I just found my Daddy. My REAL Daddy. What's my death going to do to him? I hope he's okay. I hope he knows how much I love him and always will.

_Mommy? Mommy, are you here? Please, Mommy, can you help me get back to Daddy?_

_My sweet Angel._

I turned at the sound of the voice. The familiarity of it wrapped around me like a blanket and it sounded so close, but I couldn't see her.

_Why can't I see you, Mommy?_

_You will soon enough._

_I'm… I'm not…_

_You are not._

_But where am I? And where's Daddy?_

Suddenly I felt a hand in mine and I was back in Atlantis. The infirmary to be exact. I looked up at Mom and smiled.

"I've missed you my sweet Angel."

"I've missed you too!"

We moved closer to the Daddy as he held onto my hand. He was sleeping, but it didn't look like a very peaceful rest. "I'll be back, Mary," Mom said.

As soon as she disappeared, he relaxed and there was a small smile on his face. I placed a kiss on Daddy's cheek. "I'll try not to be gone long, daddy," I whispered, "but right now I don't know how to get back. I don't think Mommy is allowed to tell me either. I'm sorry! I love you!"

"I love you, Angel," Daddy said, but he still seemed to be asleep.

* * *

Elizabeth found John exactly where Carson had left him. When she had come to check on the young girl's status, she desperately hoped to find Mary awake and John teasing her. Instead she learned from Carson that she slipped into a coma over night.

John didn't look very comfortable and she knew it was going to be next to impossible to get him up let alone out of the infirmary, but she was determined to try even if it meant making it an order. She placed a hand on his shoulder and gently shook him.

"John."

He blinked in confusion. His eyes rested on Mary for a moment, and then he turned to his left where Elizabeth was standing. "What time is it?" he asked.

"Going on 0800 now."

John sighed. Four hours. It had been four hours since Carson told him that Mary was in a coma. Fifteen hours since Mary was on the mainland chasing after Jinto. When the latter came rushing towards him and said Mary had fallen, John had been so scared.

He was even more scared when he saw his little girl's lifeless body. Now he was terrified. Terrified that he had found Mary again only to lose her. John was beginning to think that he was not allowed to be happy. That he was being punished for something. What, he didn't know.

"John," Elizabeth said. "Why don't you get something to eat? I'll sit with Mary."

"No. I don't want to leave her."

"I know you don't, but you know what you would say to Mary if she wasn't eating or if she wasn't getting any sleep. Please, John, if not for yourself, then for your daughter."

John sighed. No wonder Elizabeth was a negotiator. "Fine, but I'll be back in an hour!"

"Good," she replied, taking the now unoccupied seat.

"Thanks, Elizabeth."

"You're welcome, John."

John headed to his quarters first to take a shower. He sighed in relief as the hot water pounded his aching shoulders. He wasn't complaining, though. He would never complain about aches and pains again. Not after what his little girl had gone through.

After his shower, John changed into a pair of jeans and a t-shirt, and then headed over to the mess hall. That's where he found Rodney, Ronon, and Teyla. John grabbed a tray and something that looked suspiciously like chicken salad (although he couldn't be too sure) and joined them.

Teyla nodded at him. "John, we were going to come by and visit Mary after lunch."

He smiled sadly. "She'd like that."

"How's she doing?" Ronon asked. "Doc said something about a… coma?"

John swallowed around the lump in his throat and explained a coma as best as he could to Ronon. When the Satedan nodded in understanding, John said, "Doc's not sure if she'll wake up. At least not anytime soon."

Rodney had yet to look up or join the conversation. He had no idea why he was feeling such anger right now and he knew he shouldn't yell at anyone, most of all John, but he hated the way this conversation was going.

"Shut up!"

All three heads (and a few others) turned face him. Rodney felt like crying, but he didn't want to, especially not in front of nearly half the expedition. Before he could say anything he might regret, Rodney stood up and practically ran out of the mess hall.

John pushed his tray away and rested his head in his arms. He understood that Rodney was feeling angry about things, hell he felt just as angry that this was happening… He needed to see his friend, though. He needed to be certain he was all right.

Muttering an apology to Ronon and Teyla, John hurried off after Rodney. Teyla looked over at Ronon, who shrugged. "Let us go see Mary."

* * *

Rodney had been in his lab for about ten minutes when John came in. The scientist was sitting in the corner of the room, knees drawn up to his chest. John was a little shocked to see the tears on his friend's face.

"Rodney, I…"

"Sorry," he replied, wiping the tears. "I feel like such an idiot. I can't believe I yelled at you like that. I mean here you are trying to hold it together for your daughter and I'm blubbering like a baby."

John shook his head and sat down across from Rodney. "Stop it! You have every right to be angry and upset about this! Rodney, Mary loves you just as much as she loves me. She told me herself. You're like a second Father to her."

Rodney stared at John in complete shock. He had never even thought about being a father to anyone let alone someone who wasn't really his daughter. Rodney also never expected Mary to gravitate towards him.

"Why don't you stop in your quarters then meet me in the infirmary?"

"Yeah," Rodney replied as he watched John stand up. "Thanks."

John smiled and left the man to his thoughts. He didn't know how he sat through that conversation without breaking down into tears himself. John really knew how special Mary was after talking to Rodney McKay. Who would have thought?

When John arrived in the infirmary, all hell broke loose. He ran into Mary's room to see Carson and his team at her side. Elizabeth was standing near the door. "What's happening?" he asked shakily.

"John, I was about to call you," Elizabeth replied. "Carson said the swelling in her brain has gotten worse. They're going in to relieve the pressure."

"Mary…" John whispered. Even though he knew his friends were there for him, he couldn't help but feel so alone. He felt so helpless just like when she disappeared so long ago.

"Carson will not let her die, John," Elizabeth said.

He nodded slowly, eyes following as Carson and his team rushed her into the trauma room. John finally looked at Elizabeth. Her heart broke into pieces as she took him into her arms. Elizabeth held in her tears because right now John needed her to be strong for him.

"She'll be fine, John," Elizabeth whispered in his ear. "She's your daughter."

* * *

"Mommy! When can I go back?"

"Soon, Angel."

"But look at what this is doing to Daddy!" I exclaimed, tears falling down my cheeks. "It's so mean!"

"I know," Mommy replied.

I could tell that she was just as upset about this as I was. "Why aren't you doing anything about it? Daddy thinks I'm going to die. Please stop this, Mommy!"

Mommy knelt in front of me. "I can't do that, Angel. I'm not allowed to interfere with this. I was only allowed to come and see you and when our time was up then you would go back to Daddy."

"You sound like an Ancient," I told her, rolling my eyes. She just smiled knowingly. "Oh my God, you are?"

She ignored my statement, which to me meant yes. "I have to go my Angel. You'll wake up in a bit, as I promised."

I gave Mommy a big hug. "I love you so much!" I told her. "I'm sorry that I ran away from you and Daddy so long ago."

"Don't worry about the past so much," Mommy said. "We loved you then, we love you now and we will always love you."

She was suddenly gone and I was alone. I watched as the infirmary materialized around me. Elizabeth was holding Daddy and comforting him.

I felt the need to return to my body, but where was I? Oh, I must be in the trauma room with Carson. I'd better get in there!

* * *

Carson had just finished closing on the procedure when the warnings went off. "She's flat lining!" he cried. Before they even had a chance to charge the defibrillator, a steady beep was heard. Carson felt as though he were going to be sick.

"Oh, thank God!" Mary blinked and looked around in confusion. "It's good to see you awake. The nurses will make you comfortable while I go to your Dad. The man's probably a nervous wreck by now. We almost lost you."

"My Dad? No, Scott's not my Dad. Well, he's my adopted Dad, sure, but my real parents didn't want me."

Carson stared at her in complete shock. She didn't seem to remember the last two months since she arrived on Atlantis. Now he had to John about this and he had no clue as to how to break it to him. Sometimes he really hated his job…

Carson found John and Elizabeth sitting next to one another on the floor. The minute they heard his footsteps, they jumped up. "How is she?" John asked. Carson seemed to hesitate for a moment. "God, she's not…"

"No!" Carson said. "I'm sorry, I didn't mean to make you think that. Mary is very much alive, John. In fact she's conscious as well."

Elizabeth nodded but noticed there was something more going on. "But…?"

"But she has amnesia." He took a deep breath. "Mary doesn't remember the last two months."

"What do you mean?" John asked cautiously.

"She believes she's still with the man and woman who adopted her. She corrected me when I said her Dad was out here. She told me that Scott was her adopted Father."

John stared at Carson. This wasn't happening. It was bad enough when Mary was lying unconscious and fighting to stay alive now she couldn't even remember the last two months they had spent together.

"Is… Is this temporary?"

"I just don't know, John."

"Can I see her?"

"Of course."

John glanced at Elizabeth. "Um…"

"Of course I'll come with you, John," she replied.

John nodded thanks then entered the room. Mary was quietly resting when they came in. She eyed him in confusion. "Who are you? The doctor said he was getting Scott. Where is he?"

Elizabeth watched as all the color drained from John's face. She stepped up to Mary and smiled. "Mary, this is John, your real Father."

She shook her head. "No, that can't be…"

"Mary," Elizabeth said, pulling John closer. "You hit your head pretty hard. Dr. Beckett said you have amnesia, you've forgotten the past two months."

Elizabeth could tell John was ready to bolt from the infirmary so she kept a tight grip on his arm as she explained everything to the distraught girl. She listened, but didn't like what she was hearing.

"How can you say that about Scott and Lisa?" she exclaimed. "They took me in when my parents didn't want me!"

Mary was about to glare at the man who was supposedly her Father, but once she saw the look on his face, felt horrible for being so rude. "I'm… I'm sorry. It's just… oh, I don't know!" she said in frustration.

"It's all right," John said. "If you feel uncomfortable around me right now, I'll just leave. I've known people who had amnesia and it's no picnic."

Mary smiled slightly. "Thank you and I really am sorry!"

Elizabeth watched as John left defeated. This was going to be harder than she realized. "Mary, I'm going to try and explain everything as best as I can, although I have to admit that John should really be doing this."

"Who are you?" she asked.

"I'm sorry," Elizabeth replied. "I'm Dr. Elizabeth Weir. Your friend's brother found information on your birth Father and you contacted someone who could help you find him…"

* * *

Rodney found John on the balcony in the infirmary. His back was against the wall and he was staring out at the water. Rodney could swear he saw tears in his eyes. "Hey," he said, sitting next to him.

"Carson tell you?"

"Yeah. What I want to know is why you aren't in there helping Mary remember. I think you of all people should be doing that."

John shook his head. "She's not comfortable with me in there. She kept asking for Scott, she said that was her Dad and she loved him. If only she knew what he did to us. To her!"

"She's not going to know it if you just sit on your ass pitying yourself!" Rodney exclaimed. "You need to think of what's best for Mary!"

John couldn't believe he was getting advice on children from Rodney McKay and Rodney couldn't believe he was giving it. "Whatever works," Rodney muttered as John stood up and headed back inside.

Mary had just fallen asleep when John appeared. Elizabeth looked up from the book she was reading. "How are you holding up?" she asked.

"Okay. I guess I was stupid for just leaving Mary like that even if she was a little uncomfortable."

Elizabeth shook her head. "Not entirely stupid, John. If I were you I would have been just as uncomfortable especially giving what you have to tell her."

"You mean..." John trailed off as Elizabeth gave him a look. Of course she didn't tell Mary everything. It was his responsibility and he was going to have to face it head on. He cleared his throat. "Mind if I sit with her?"

"Not at all," she replied. "Carson said she should be out for the rest of the night, though. He had another bed moved in for you earlier."

John nodded. "Thanks, Elizabeth. For everything."

"You're welcome, John."

* * *

Mary woke up and looked to her right. She smiled, happy to see her Dad again. She didn't have the heart to wake him, but knew what he had gone through while she was in her coma.

"Daddy."

John blinked and glanced to his right. "Mary?" he said uncertainly as he sat up from his slouched position.

She giggled. "Yeah, who else would I be?"

John immediately rushed over, hugging her close. "Angel, I'm so happy you remember me."

"What are you talking about?"

"You had amnesia, Mary. You couldn't remember what happened in the last two months."

Mary couldn't believe what she was hearing. How could that have happened? She didn't know, but she was very glad that she seemed to have her memories back. "Daddy, I saw Mommy."

Now it was John's turn to ask what she meant.

"I was... out of my body, or something like that. Mommy came to me. She told me how much she loved us and missed us. She wanted you to know that she loves you so much, Daddy."

* * *

One week later Mary was discharged from the infirmary. She was heading up to Elizabeth's office when Rodney stopped her. "Hi, Dr. McKay!" she said with a smile.

"Hi. How are you feeling?"

"Great, thanks." She could tell he seemed almost thoughtful. "What's wrong?"

Mary suddenly found herself wrapped in the arms of Rodney McKay. "I am so glad you're all right!" he exclaimed. Rodney bent down, kissed her cheek, and ran off down the hall.

Mary laughed and again headed towards her destination. She loved everyone on Atlantis. They were wonderful and caring people. Mary smiled in greeting at the people walking past her. It certainly felt good to be alive.

"Buon giorno," Mary said as she knocked on the door to Elizabeth's office.

"Buon giorno. Come sta?"

"Va bene cosi."

"Hey, no fair speaking Italian in front of me!" John said with a pout.

Mary and Elizabeth grinned at one another as they began speaking again. John had no idea what they were saying, but he saw Elizabeth blushing a bright red.

"What?" he asked.

The two just laughed leaving a confused John Sheppard in their wake.

* * *

Translations:  
Buon giorno - good morning  
Come sta - how are you  
Va bene cosi - just fine 


End file.
